PDB Structure Viewer

PDB ID: 5LF3

Title: HUMAN 20S PROTEASOME COMPLEX WITH BORTEZOMIB AT 2.1 ANGSTROM

Experimental Method: X-RAY DIFFRACTION

Resolution: 2.10 Å

Ligands: 1PE, 6V1, BO2, CL, K, MG, YCM

Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b

Viewer size: 800 x 600

Chain style: {'stick': {}}

Residue style: {'stick': {'colorscheme': 'cyanCarbon'}}

Generated: 2025-07-03 23:01:35

Script: binding_visualizer.py

Config file: binding_visualizer.yaml

Python version: 3.9.6

Platform: Darwin 24.5.0

User/Host: andreazedda@Andreas-MacBook-Pro.local

PDB Downloaded: 2025-07-03 21:01:32 UTC

Script SHA256: 9b794f86511be876a9a3c87c13b38ff50f8484e67cfb4035c7c032f7ff378418

Config SHA256: 616711b129618b4886590e47cf58d8619f5b7fa6314f0a9e4e95f2818c54e4b8

Instructions: Drag to rotate, scroll to zoom, double-click to center. Hover over atoms for details.

Dependencies: py3Dmol 2.4.0, requests 2.32.3, pyyaml 6.0.2

Git commit: 7b491d9

Downloads: PDB file | YAML config

Show YAML Config

pdb_id: "5LF3"
viewer:
  width: 800
  height: 600
visualization:
  chain_style: 
    stick: {}
  residue_style:
    stick: 
      colorscheme: "cyanCarbon"
ligand: "BOR"      # Main drug/ligand to map

# PDF Report Generation
generate_pdf: true
pdf_options:
  include_structure_image: true
  image_width: 800
  image_height: 600
  cleanup_aux_files: true

binding_site_detection:
  enabled: true    # Switch for biopython residue mapping
  cutoff_angstrom: 5.0

mutations:
  - chain: K
    resnum: 45
    mutation: A45T
    effect: resistance
  - chain: K
    resnum: 49
    mutation: C49W
    effect: unknown

therapies:
  - name: Bortezomib
    pdb_ligand: BOR
    clinical_phase: Approved
    mechanism: Proteasome inhibitor targeting the 26S proteasome
    mm_relevance: High
    resistance_mutations: [A45T, C49W]
  - name: Carfilzomib
    pdb_ligand: ...
    clinical_phase: Approved
    mm_relevance: High
    resistance_mutations: [...]

pathways:
  - name: "Proteasome pathway"
    kegg_id: "hsa03050"
    reactome_id: "R-HSA-174084"

literature:
  - doi: "10.1126/science.aaf8993"
    pmid: "27493187"
    title: "The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design."

Citation: The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design.

Chain	ResNum	Mutation	Effect
K	45	A45T	resistance
K	49	C49W	unknown

Name	Ligand	Phase	MM Relevance	Resistance Mutations
Bortezomib	BOR	Approved	High	A45T, C49W
Carfilzomib	...	Approved	High	...

Proteasome pathway hsa03050 R-HSA-174084

The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design. 10.1126/science.aaf8993 27493187

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